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(-) Description

Title :  OXIDIZED YFIR
 
Authors :  M. Xu, T. Jiang
Date :  09 Mar 15  (Deposition) - 22 Apr 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Periplasmic Repressor Protein, Oxidized Form (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Yang, X. -A. Yang, M. Xu, L. Zhou, Z. Fan, T. Jiang
Crystal Structures Of Yfir From Pseudomonas Aeruginosa In Two Redox States
Biochem. Biophys. Res. Commun. V. 461 14 2015
PubMed-ID: 25849887  |  Reference-DOI: 10.1016/J.BBRC.2015.03.160

(-) Compounds

Molecule 1 - YFIR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 35-190
    Gene: YFIR, PA1121
    Organism Scientific: PSEUDOMONAS AERUGINOSA PAO1
    Organism Taxid: 208964
    Strain: PAO1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:41 , ARG B:99 , ALA B:100 , ASN B:103binding site for residue SO4 B 201
2AC2SOFTWAREARG A:99 , ALA A:100 , ASN A:103 , THR B:39 , SER B:40 , ILE B:41binding site for residue SO4 B 202

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:71 -A:110
2A:145 -A:152
3B:71 -B:110
4B:145 -B:152
5C:71 -C:110
6C:145 -C:152
7D:71 -D:110
8D:145 -D:152

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YNA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YNA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YNA)

(-) Exons   (0, 0)

(no "Exon" information available for 4YNA)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.ee.......eeeeee.....hhhhhh.ee.....eeeeeee.....hhhhhh.eeee...hhhhhhhhhhhh.....eeee...hhhhhh..eeee......eeeehhhhhhhhh.ee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yna A  38 RTSIEQRSNAVSQVLLGIFSYVRWPKEPAVLQLCVVGPTEYADGLLRGMVQANGRRVHAERRAVDNPDLGTLCNVIYLGVVDERERQQVFRSLAGHPVLSISERGTECSVGSMFCLNVGGPRITFEANLDSIARSGVRVHPSVLKLARRQATP 190
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187   


Chain B from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.ee......eeeeeee.....hhhhhh.ee.....eeeeee......hhhhhh.eeee...hhhhhhhhhhhhh....eeee...........eeee......eeeehhhhhhhh..ee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yna B  38 RTSIEQRSNAVSQVLLGIFSYVRWPKEPAVLQLCVVGPTEYADGLLRGMVQANGRRVHAERRAVDNPDLGTLCNVIYLGVVDERERQQVFRSLAGHPVLSISERGTECSVGSMFCLNVGGPRITFEANLDSIARSGVRVHPSVLKLAR 185
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177        


Chain C from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhee.......eeeeee.....hhhhhh.ee.....eeeeeee.....hhhhhh.eeee...hhhhhhhhhhhh.....eeee...hhhhh...eeee......eeeehhhhhhhhh.ee...hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yna C  39 TSIEQRSNAVSQVLLGIFSYVRWPKEPAVLQLCVVGPTEYADGLLRGMVQANGRRVHAERRAVDNPDLGTLCNVIYLGVVDERERQQVFRSLAGHPVLSISERGTECSVGSMFCLNVGGPRITFEANLDSIARSGVRVHPSVLKLARRQ 187
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178         


Chain D from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhee......eeeeeee.....hhhhhh.ee.....eeeeee......hhhhhh.eeee...hhhhhhhhhhhhh....eeee...........eeee......eeee..hhhhhh..ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yna D  38 RTSIEQRSNAVSQVLLGIFSYVRWPKEPAVLQLCVVGPTEYADGLLRGMVQANGRRVHAERRAVDNPDLGTLCNVIYLGVVDERERQQVFRSLAGHPVLSISERGTECSVGSMFCLNVGGPRITFEANLDSIARSGVRVHPSVLK 182
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4YNA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YNA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YNA)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4YNA)

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  4yna
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        Q9I4L4_PSEAE | Q9I4L4: 4xjy 4yn7 4yn9 4zhu 4zhy 5eb1 5eb2 5eb3

(-) Related Entries Specified in the PDB File

4yn7 4yn9